[SOLVED] Animation issue Error in phase 3 of MOR plugin. Please Help!

[Pasquale94]

Hello Sofa Forum,
I am a pneumatic actuator (just one air chamber so very simple) that i want to reduce of order.
So i am using on Ubuntu 20.04 Sofa 20.04 with python 2.7 and I arrived to write the code ModelOrderReduction.py like this, folowing the tutorial in online documentation:

 Import
import os
import sys

sys.path.append(os.getcwd()+'/../python')

# MOR IMPORT
from mor.gui import utility
from mor.reduction import ReduceModel
from mor.reduction.container import ObjToAnimate

# Important path
from PyQt4 import QtCore, QtGui
app = QtGui.QApplication(sys.argv)

originalScene = utility.openFileName('Select the SOFA scene you want to reduce')
#meshes = utility.openFilesNames('Select the meshes & visual of your scene')
outputDir = utility.openDirName('Select the directory tha will contain all the results')

# if you haven't install PyQt the previous function won't work
# As an alternative you can enter the absolute path to the conresponding files directly:
# originalScene = /PathToMy/Original/Scene

nodesToReduce_finger = '/finger'
cavity = ObjToAnimate("finger/cavity", incr=5e-6,incrPeriod=0.001,rangeOfAction=0.0483)
listObjToAnimate_finger = [cavity]

addRigidBodyModes_finger = [0,0,0]
tolModes = 0.001

# Tolerance
tolGIE =  0.05

# Optionnal
verbose = False
nbrCPU = 4
packageName = 'test'
addToLib = False

# Initialization of our script
nodesToReduce = nodesToReduce_finger # nodesToReduce_STARFISH
listObjToAnimate = listObjToAnimate_finger # listObjToAnimate_STARFISH
addRigidBodyModes = addRigidBodyModes_finger # addRigidBodyModes_STARFISH

reduceMyModel = ReduceModel(    originalScene,  
                                nodesToReduce,
                                listObjToAnimate,
                                tolModes,tolGIE,
                                outputDir,
                                packageName = packageName,
                                addToLib = addToLib,
                                verbose = verbose,
                                addRigidBodyModes = addRigidBodyModes)

reduceMyModel.phase1()
reduceMyModel.phase2()
reduceMyModel.phase3()

I have a problem in the phase 3, in the terminal is present all this output:

periodSaveGIE : 6 | nbTrainingSet : 9660 | nbIterations : 9
##################################################
[140573650081536] processing threaded sofa task in: /tmp/sofa-launcher-WoW6ZK/phase1_snapshots.py
[140573658830592] processing threaded sofa task in: /tmp/sofa-launcher-ulwwu7/phase1_snapshots.py
PHASE 1 --- 14.8335149288 seconds ---
###################################################
Executing readStateFilesAndComputeModes.py

Arguments :

     INPUT  :
     in stateFilePath         : /home/pasquale/sofa-new-python2/src/applications/plugins/ModelOrderReduction/python/Thick_finger/debug/stateFile.state
     with arguments           :
         -tolerance               : 0.001 

     OUTPUT :
         -modesFileName           : /home/pasquale/sofa-new-python2/src/applications/plugins/ModelOrderReduction/python/Thick_finger/data/modes.txt 

###################################################
16 possible modes with a tolerance of 0.001
PHASE 2 --- 0.348403930664 seconds ---
[140574291900160] processing threaded sofa task in: /tmp/sofa-launcher-0_5r9P/phase2_prepareECSW.py
[140573163906816] processing threaded sofa task in: /tmp/sofa-launcher-za7OcM/phase2_prepareECSW.py
IOError : there is no /tmp/sofa-launcher-0_5r9P/elmts_finger.txt , check the template log to find why.
Here some clue for its probable origin :    - Your animation arguments are incorrect and it hasn't find anything to animate
Traceback (most recent call last):
  File "ModelOrderReduction.py", line 68, in <module>
    reduceMyModel.phase3()
  File "/home/pasquale/sofa-new-python2/src/applications/plugins/ModelOrderReduction/python/mor/reduction/reduceModel.py", line 379, in phase3
    self.reductionParam.massName = glob.glob(results[self.phaseToSaveIndex]["directory"]+slash+"*_reduced.txt")[0]
IndexError: list index out of range

I checked also in the relative output.log generated by the sofa launcher and the only error that i have is this:

[ERROR]   [PythonScript] RuntimeError: Unable to create 'reducedFF_finger_0' of type 'HyperReducedTetrahedronHyperelasticityFEMForceField' in node 'finger'. Object type HyperReducedTetrahedronHyperelasticityFEMForceField<Vec3d> was not created  
 The object is not in the factory.  

  File "phase2_prepareECSW.py", line 43, in createScene
    phase1_snapshots.createScene(Wrapper(rootNode, replaceAndSave.MORreplace, paramWrapper))
  File "phase1_snapshots.py", line 44, in createScene
    originalScene.createScene(rootNode)
  File "/home/pasquale/sofa-new-python2/src/applications/plugins/ModelOrderReduction/python/Thick_finger/thicker_finger.py", line 43, in createScene
    finger.createObject('TetrahedronHyperelasticityFEMForceField', template='Vec3f', name='FEM', src ='@topo', ParameterSet=str(mu)+' '+str(k0),materialName="NeoHookean")
  File "/home/pasquale/sofa-new-python2/src/applications/plugins/STLIB/python/stlib/scene/wrapper.py", line 35, in createObject
    return self.node.createObject(objectArg[0], **objectArg[1])

But is strange for me because i compiled the plugin so I don’t understand why the object is not in the factory.

I already know that @olivier-goury and @felixvanneste work on this plugin, also form other answers in the topic , so i tag directly them hope they can help me.
Thanks a lot in advance.

[Félix]

Hello @pasquale94,

The easiest way to help you, I think, is that you give us your scene and I will do a quick test with it.

But at first glance it seems that it cannot instantiate a component from the plugin MOR. So maybe it cannot load the plugin for some reason…

Hope it help !

Have a good day,
Félix

[Pasquale94]

Hello @felixvanneste ,

Is good for you if I contact you by email sending the scene?

Many Thanks for the help!

Pasquale

[Pasquale94]

Hello @felixvanneste ,

i created a github repo, so you can dowload the files, the scene is thicker_finger.py

Thanks again!

During the installation of MOR plugin I had problem with Sofa.Gl library apparently in my sofa 20.12 (ubuntu version) is not present.
Maybe this can be the origin of the issue.

[Pasquale94]

Hello @felixvanneste

Do you have some updates?

Thanks for the help!

[Félix]

Hello @pasquale94,

they were multiple errors some from the plugin itself and some from your scene.

Concerning your scene:

– you need to add the plugin ModelOrderReduction in your initial scene, I need to add that fact into the documentation…
– use GenericConstraintSolver instead of LinearSolverConstraintCorrection, it seems there is problem with linearSolvers and mor component I also need to add that to the doc…

For the reduction:

– you were putting incrPeriod=0.001 but I made a mistake in the documentation, its not the period but the number of dt between each animation. So here I guess you want one to animate each dt then incrPeriod=1.
– I have made some small modification in the python code to correct some issue, please copy/paste or pull to have the update.

In the end I have something like that:

cavity = ObjToAnimate("finger/cavity", incr=5e-4,incrPeriod=1,rangeOfAction=0.1)
listObjToAnimate = [cavity]
addRigidBodyModes = [0,0,0]

# Tolerance
tolModes = 0.001
tolGIE =  0.05

# Optional
verbose = True
nbrCPU = 4

packageName = 'test'
addToLib = False

reduceMyModel = ReduceModel(    originalScene,  
                                nodeToReduce,
                                listObjToAnimate,
                                tolModes,tolGIE,
                                outputDir,
                                phaseToSave=[1],
                                packageName = packageName,
                                addToLib = addToLib,
                                verbose = verbose,
                                addRigidBodyModes = addRigidBodyModes)

reduceMyModel.phase1(phasesToExecute = [1])
reduceMyModel.phase2()
reduceMyModel.phase3(phasesToExecute = [1])
reduceMyModel.phase4()

I hope this help and thanks for the feed back!

[Félix]

Lat thing, if you don’t know.
When you do phase 1 & 3 it generate some stateFile.state that you can check by launching the debug/debug_scene.py.
It will show you what happened during the scene execution allowing you to see if the animation function you use do the job.

[Pasquale94]

Hello @felixvanneste,

I applied your modifications, but using the Generic Constraint solver the finger is not animated (seen in the debug scene).

Anyway using both Linear or Generic Solvers I have always this error when the phase2 starts:

Executing readStateFilesAndComputeModes.py

Arguments :

     INPUT  :
     in stateFilePath         : /home/pasquale/sofa-new-python2/src/applications/plugins/ModelOrderReduction/python/Thick_finger/debug/stateFile.state
     with arguments           :
         -tolerance               : 0.001 

     OUTPUT :
         -modesFileName           : /home/pasquale/sofa-new-python2/src/applications/plugins/ModelOrderReduction/python/Thick_finger/data/modes.txt 

###################################################
Reading file '/home/pasquale/sofa-new-python2/src/applications/plugins/ModelOrderReduction/python/Thick_finger/debug/stateFile.state':
XO NOT FOUND
Traceback (most recent call last):
  File "ModelOrderReduction.py", line 68, in <module>
    reduceMyModel.phase2()
  File "/home/pasquale/sofa-new-python2/src/applications/plugins/ModelOrderReduction/python/mor/reduction/reduceModel.py", line 294, in phase2
    raise ValueError("problem of execution of readStateFilesAndComputeModes")
ValueError: problem of execution of readStateFilesAndComputeModes

What does it mean? Then I seen that the file stateFile.state in debug folder starts from a T = 6 while i would expect that was T = 0 as first increment.

Thank you for the help. Do you had the same error with my scene?

[Félix]

Hello @pasquale94,

I am really sorry I forget to tell you that you need to put absolute path into your scene…

import Sofa
import os
path = os.path.dirname(os.path.abspath(__file__))+'/design/'

def createScene(rootNode):

	rootNode.createObject('RequiredPlugin', pluginName='SoftRobots SofaPython SofaOpenglVisual SofaSparseSolver SofaPreconditioner SofaMiscCollision SofaExporter ModelOrderReduction SofaMiscFem SofaMiscForceField')
	rootNode.createObject('VisualStyle') #, displayFlags='showVisualModels showBehaviorModels hideCollisionModels hideBoundingCollisionModels showForceFields hideInteractionForceFields hideWireframe')
	rootNode.findData('gravity').value=[ 0, 0, -9810]
	rootNode.findData('dt').value = 0.001
	rootNode.createObject('FreeMotionAnimationLoop')
	rootNode.createObject('GenericConstraintSolver', tolerance=1e-12, maxIterations=10000)
	rootNode.createObject('DefaultPipeline')
	rootNode.createObject('BruteForceDetection')
	rootNode.createObject('DefaultContactManager', response='FrictionContact', responseParams='mu=0.6')
	rootNode.createObject('LocalMinDistance', name='Proximity', alarmDistance=5, contactDistance=1, angleCone=0.0)
	rootNode.createObject('BackgroundSetting', color=[0, 0.168627, 0.211765])
	rootNode.createObject('OglSceneFrame', style='Arrows', alignment='TopRight')
	#rootNode.createObject('PythonScriptController', filename='pythonControllers/fingerController.py', classname = 'FingerController')

	finger = rootNode.createChild('finger')
	finger.createObject('EulerImplicitSolver', name='odesolver', rayleighStiffness=0.1, rayleighMass=0.1)
	finger.createObject('SparseLDLSolver', name='directSolver')
	finger.createObject('MeshVTKLoader', name='loader', filename=path+'finger0.vtu')
	finger.createObject('MechanicalObject', name='tetras', template='Vec3d', src = '@loader')
	finger.createObject('TetrahedronSetTopologyContainer', name="topo", src ='@loader')
	finger.createObject('TetrahedronSetTopologyModifier' ,  name="Modifier")
	#finger.createObject('TetrahedronSetTopologyAlgorithms', name="TopoAlgo", template="Vec3d")
	finger.createObject('TetrahedronSetGeometryAlgorithms', template="Vec3d" ,name="GeomAlgo")#, drawTriangles="1")
	

	finger.createObject('MeshMatrixMass', massDensity='1.020e-9', src = '@topo')

	#youngModulus = 120
	#poisson = 0.44
	mu = 2*109
	k0 = 1/1.150e-2

	finger.createObject('TetrahedronHyperelasticityFEMForceField', template='Vec3d', name='FEM', src ='@topo', ParameterSet=str(mu)+' '+str(k0),materialName="NeoHookean")
	#finger.createObject('TetrahedronFEMForceField', template='Vec3d', name='FEM', src ='@topo', youngModulus = 120, poisson = 0.44)
	finger.createObject('BoxROI', name='boxROI', box=[-10, 0, 0, 10,15, 5], drawBoxes=True)
	finger.createObject('RestShapeSpringsForceField', points='@boxROI.indices', stiffness=1e12, angularStiffness=1e12)
	# finger.createObject('LinearSolverConstraintCorrection', solverName='directSolver')
	finger.createObject('GenericConstraintCorrection', solverName='directSolver')

	cavity = finger.createChild('cavity')
	cavity.createObject('MeshObjLoader', name='cavityLoader', filename=path+'BSPA_New_Design_Inner.obj')
	cavity.createObject('MeshTopology', src='@cavityLoader', name='cavityMesh')
	cavity.createObject('MechanicalObject', name='cavity')
	cavity.createObject('SurfacePressureConstraint', name='SurfacePressureConstraint', template='Vec3d', value= 0, triangles='@cavityMesh.triangles', valueType='pressure')
	cavity.createObject('BarycentricMapping', name='mapping', mapForces=False, mapMasses=False)

	collisionFinger = finger.createChild('collisionFinger')
	collisionFinger.createObject('MeshObjLoader', name='loader', filename=path+'BSPA_New_Design_Outer.obj')
	collisionFinger.createObject('MeshTopology', src='@loader', name='topo')
	collisionFinger.createObject('MechanicalObject', name='collisMech')
	collisionFinger.createObject('TriangleCollisionModel', selfCollision=False)
	collisionFinger.createObject('LineCollisionModel', selfCollision=False)
	collisionFinger.createObject('PointCollisionModel', selfCollision=False)
	collisionFinger.createObject('BarycentricMapping')

	modelVisu = finger.createChild('visu')
	modelVisu.createObject('MeshObjLoader', name='loader', filename=path+'BSPA_New_Design_Outer.obj')
	modelVisu.createObject('OglModel', src='@loader', color='yellow')
	modelVisu.createObject('BarycentricMapping')

	return rootNode

Also for the XO NOT FOUND issue if you haven’t pull my recent changes and used what I have put above its normal.
But if you don’t want to complicate yourself you can do it like that:

cavity = ObjToAnimate("finger/cavity", incr=5e-4,incrPeriod=1,rangeOfAction=0.1)
listObjToAnimate = [cavity]
addRigidBodyModes = [0,0,0]

# Tolerance
tolModes = 0.001
tolGIE =  0.05

# Optional
verbose = True
nbrCPU = 4

packageName = 'test'
addToLib = False

reduceMyModel = ReduceModel(    originalScene,  
                                nodeToReduce,
                                listObjToAnimate,
                                tolModes,tolGIE,
                                outputDir,
                                packageName = packageName,
                                addToLib = addToLib,
                                verbose = verbose,
                                addRigidBodyModes = addRigidBodyModes)

reduceMyModel.phase1()
reduceMyModel.phase2()
reduceMyModel.phase3()
reduceMyModel.phase4()

I hope it solve your problems…
Sorry for the inconvenience, some work still need to be done with the documentation to help debug/avoid some little mistake.

[Pasquale94]

Hello @felixvanneste,

Now the code produce the reduced_test.py scene, but when i launch the scene in sofa it don’t actuate the pneunet.

So I have to add a python controller to the scene?

Thanks a lot for the help!

[Félix]

Hey again @pasquale94,

Yes if everything works fine, the plugin only generate a python file that you can re-use as a module.
It contains a function with some basic parameters that instantiate the reduced model of the node you give as an argument to nodeToReduce.

Doesn’t seems really clear so here an example :

 
import Sofa
import os
path = os.path.dirname(os.path.abspath(__file__))+'/design/'

from reduced_test import Reduced_test

def createScene(rootNode):

    rootNode.createObject('RequiredPlugin', pluginName='SoftRobots SofaPython SofaOpenglVisual SofaSparseSolver SofaPreconditioner SofaMiscCollision SofaExporter ModelOrderReduction SofaMiscFem SofaMiscForceField')
    rootNode.createObject('VisualStyle')
    rootNode.findData('gravity').value=[ 0, 0, -9810]
    rootNode.findData('dt').value = 0.001
    rootNode.createObject('FreeMotionAnimationLoop')
    rootNode.createObject('GenericConstraintSolver', tolerance=1e-12, maxIterations=10000)
    rootNode.createObject('DefaultPipeline')
    rootNode.createObject('BruteForceDetection')
    rootNode.createObject('DefaultContactManager', response='FrictionContact', responseParams='mu=0.6')
    rootNode.createObject('LocalMinDistance', name='Proximity', alarmDistance=5, contactDistance=1, angleCone=0.0)
    rootNode.createObject('BackgroundSetting', color=[0, 0.168627, 0.211765])
    rootNode.createObject('OglSceneFrame', style='Arrows', alignment='TopRight')

    # ADD your controller
    rootNode.createObject('PythonScriptController', filename='pythonControllers/fingerController.py', classname = 'FingerController')

    # ADD your reduced model
    Reduced_test(attachedTo=rootNode,name="Reduced_test",rotation=[0.0, 0.0, 0.0],translation=[0.0, 0.0, 0.0],scale=[1.0, 1.0, 1.0],
                surfaceMeshFileName=False,surfaceColor=[1.0, 1.0, 1.0],nbrOfModes=3,hyperReduction=True)

[Pasquale94]

Hello @felixvanneste .

This is the last question then i will close the topic ahah. Thanjks for your help.

Once I produced the reduced_scene, can i integer the scene in a Python 3 scripting?
Or I have to use always a scene coded in python 2?

Thank you for the help.

[Félix]

Hello @pasquale94,

no problem I am happy to help you use it !

Yes you can adjust the scene to make it work for python3.
There are no problems for the c++ mor components to work with python3, its just that the interface I have developed to ease the reduction process is (for the moment) only working with python2…

A last remark, when I had reduced your scene last Monday I have noted that even reduced your scene was kind of slow and its probably due to your visual mesh which seems to be maybe too precise for the purpose of a visual model.

[Pasquale94]

Hello @felixvanneste,
Thanks for all the help and advice.

I will close the topic, the issue is solved.

[Author]

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